openMetadataInitiative / openMINDS_instances

Well defined metadata instances for selected schemas of the openMINDS metadata models.
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New 'technique' suggestions #103

Open archgogo opened 2 years ago

archgogo commented 2 years ago

We forward these term suggestions that EBRAINS received from data providers: <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

name | suggestedTerminology | interlex ID | Notes | definition -- | -- | -- | -- | -- Cryoprotection | technique |   |   |   tissue sectioning | technique |   | terms like cryosectioning, vibratome sectioning, etc exist as CT and maybe this can be an overarching term including all of them. [ONE TERM TO RULE THEM ALL!] |   counterstaining | technique |   | also a term that could include other terms like H&E stain.. |   manual correction | technique |   | I am not sure if the suggested definition is irght. |   feature extraction | technique | http://uri.interlex.org/base/ilx_0779786 |   | A planed process with objective of obtaining quantified values from an image. slow receptor inhibition | technique |   |   |   fast receptor inhibition | technique |   |   |   volume fraction estimation | technique |   |   | estimating volume fraction of each element by point counting in serial semithin sections applying the Cavalieri’s principle movie occlusion paradigm (Muckli, et al. 2019) | technique |   |   | Paradigm displaying occluded scenes to subjects to investigate cortical connections thionin staining | technique |   |   | This stain is specific for DNA and Nissl substance, which is primarily ribosomal RNA. Thionin binds to acidic proteins and nucleic acids with a specificity determined by the pH of the final staining solution. deep brain stimulation | technique | http://uri.interlex.org/base/ilx_0102970 |   | A surgical treatment involving the implantation of a medical device called a brain pacemaker, which sends electrical impulses to specific parts of the brain. BOLD signal | technique (if written as BOLD MRI) | http://uri.interlex.org/base/ilx_0739352 |   | A magnetic resonance imaging technique that uses the difference between the magnetic signals of hemoglobin when it is carrying oxygen (oxyhemoglobin) and when it is not carrying oxygen (deoxyhemoglobin) to detect metabolic activity, and hence neurologic activity, in the brain. perturbed activation | Technique or semanticDataType (stimulatedData) |   |   | The definition on KG might be wrong. As I undertsand it is Perturbation of brain activity medical diagnosis | technique or subjectAttribute | http://uri.interlex.org/base/ilx_0778153 |   |  

lzehl commented 2 years ago

@archgogo thank you for bringing this up. Could we leave out the linkages to the EBRAINS KG Editor though? We can keep track of them elsewhere since this is a public repository and the linkages are not accessible for any openMINDS partner/contributor that is working outside of the EBRAINS curation team

archgogo commented 2 years ago

Hi @lzehl , sure, I will edit the issue to remove the links :)

UlrikeS91 commented 2 years ago
My feedback to the list: term add as technique? reason
Cryoprotection  yes
tissue sectioning yes
counterstaining maybe This would need to be discussed if and how we would like to add this.
manual correction yes I think this is a term we got from @tgbugs some time back in relation to preprocessing of images to make the images look nicer
feature extraction yes
slow receptor inhibition no This is the outcome, I assume the technique was some sort of treatment ("drug administration" or "drug application" or similar?)
fast receptor inhibition no same as above
volume fraction estimation yes? not an expert but we have other "estimation" techniques, sounds reasonable to me
movie occlusion paradigm (Muckli, et al. 2019) no this is a behavioral protocol, there might be techniques involved but the term itself is not one
thionin staining maybe thionin is a Nissl staining, I think we decided to stick to Nissl for those cases because the staining agent is a parameter to achieve Nissl staining; we could reconsider @lzehl?
deep brain stimulation not sure totally outside of my expertise, @lzehl?
BOLD signal no? not an expert but I think it is an fMRI setting or similar, @lzehl how would we capture this?
perturbed activation no? not an expert but it feels wrong, @apdavison maybe knows where this could belong?
medical diagnosis maybe diagnosis is the end result, maybe as "diagnostic testing" or simply " diagnostic technique"?
lzehl commented 5 months ago

@UlrikeS91 @tgbugs let's discuss the list in the next meeting. My assessment would be (not fully done yet):

ADD:

UNCLEAR: